Ah, sorry - when you said it was showing as drops I thought you meant the Get Latest tab wanted to drop them from your local DB.
If they are listed as Adds, then yes, it does sound like previous commits didn't get rid of them for some reason. Seems a little odd, if there was a problem deleting the file I would have expected an error to be thrown.
One workaround, depending on the number of objects, would be to delete the files manually from your Repo (using Tortoise for example, if you're working with SVN) and refreshing.
Failing that, if you're happy your local DB is up-to-date you could remove the folder completely from your repo, recreate it, then perform an "initial" commit again.